--- Rachel Alcraft, Bioinformatics ---

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Bioinformatics Code

These projects have been developed as a result of studying Bioinformatics at Birkbeck College, UK

Protein Structure Utility - Birkbeck MSc

This website and database was developed as part of an MSc thesis in Bioinformatics and Systems Biology (2020)
The database contains 3434 high resolution structures with resolution <= 1.3Å and 2697 structures from 2019 > 1.3Å
The website allows production of geometric plots and statistical analyses using these structures and selected criteria.
A highlight is the demonstration of the bimodal nature of tau.

PSU Birkbeck help and documentation is here
The Website hosted on the Birkbeck College servers is here

PsuGeometry

This is a python library to produce geoemntric analyses of protein structures, including the secondary structure information from dssp and the electron density information from ccp4 files where available. The images produced range from a simple Ramachandran plot than can be coloured on for example secondary structure, electron density or B-Factor, to say, a correlation of number of electrons against B-Factor. The library contains some pre-created reports so the code to create seom fairly involved reports is minimal.

PsuGeometry help and documentation is here

PsuDensity

This is a python library to analyse the electron density of protein structures directly, including the ability to calculate the second derivative of the electron density. The images are produced as planar slices based on 3 given xyz coordinates for a central atom, a linear atom and a planar atom. The PsuGeometry library is used to create html reports in a consistent format, enabling slices at different sizes and granularity, different interpolation methods, derivations as far as the degree of the interpolation, and any combination of Fo and Fc (based on an assumption of the underlying matrices as 2Fo-Fc and Fo-Fc).

PsuDensity help and documentation is here

Density Flight

Density Flight is a windows application to view the inside of an electron density matrix. The application allows you to navigate around like a flight simulator, viewing atoms, bonds between atoms, finding density peaks, rotateing in the space to seek planar atoms.
The application can currently be downloaded from github and built in Vsiual Studio 2019 (C#)
It will be available for beta testing shortly on request.

Density Flight help and documentation is here

PsuGeometry Example

These links show some examples of images and reports produced by PsuGeometry:

• Cryo EM examples:
• Data and density:
• Correlations:
• Matching ProCheck:

Density Peaks and Atoms Comparison

PSU: Geometric Correlations

Row 8
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Contact Rachel Alcraft by email, (Rachel's email)
Return to Rachel's home page - rachelalcraft.github.io
For notes on citations for this work click here